Difference between revisions of "FlyBase:About"

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     Gillian Millburn
 
     Gillian Millburn
 
     Laura Ponting
 
     Laura Ponting
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    David Osumi-Sutherland
 
 
     Ray Stefancsik
 
     Ray Stefancsik
 
     Susan Tweedie
 
     Susan Tweedie
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     Richard Cripps (PI)
 
     Richard Cripps (PI)
 
     Harriett Platero
 
     Harriett Platero
−
 
  
 
==FlyBase Publications==
 
==FlyBase Publications==

Revision as of 16:08, 4 September 2013

FlyBase Consortium

The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico.

Please use the contact FlyBase form to write to us.

FlyBase-Harvard
Biological Laboratories, Harvard University
16 Divinity Avenue
Cambridge, Massachusetts 02138
USA
   William Gelbart (PI)
   Kris Broll
   Lynn Crosby
   Gil dos Santos
   David Emmert
   L. Sian Gramates
   Kathleen Falls
   Beverley Matthews
   Susan Russo
   Andy Schroeder
   Susan St. Pierre
   Pinglei Zhou
   Mark Zytkovicz
FlyBase-Cambridge
Department of Genetics, University of Cambridge
Downing Street, Cambridge CB2 3EH
UK
   Nick Brown (PI)
   Boris Adryan
   Helen Attrill
   Marta Costa
   Steven Marygold
   Peter McQuilton
   Gillian Millburn
   Laura Ponting
   Ray Stefancsik
   Susan Tweedie
FlyBase-Indiana
Department of Biology, Indiana University
1001 East 3rd Street
Bloomington, Indiana 47405-7005
USA
   Thomas Kaufman (PI)
   Kathy Matthews (PI)
   Josh Goodman
   Gary Grumbling
   Victor Strelets
   Jim Thurmond
FlyBase-NewMexico
Department of Biology, Castetter Hall - Room 200
University of New Mexico,
Albuquerque, New Mexico 87131
USA
   Maggie Werner-Washburne (PI)
   Richard Cripps (PI)
   Harriett Platero

FlyBase Publications

S.J. Marygold, P.C. Leyland, R.L. Seal, J.L. Goodman, J.R. Thurmond, V.B. Strelets, R.J. Wilson and the FlyBase Consortium (2013).
FlyBase: improvements to the bibliography.
Nucleic Acids Res. 41(D1):D751-D757. [FBrf0220350]


Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV. (2013).
Systematic analysis of experimental phenotype data reveals gene functions.
PLoS One. 8(4):e60847. PMID: 23626672


McQuilton P and the FlyBase Consortium (2012).
Opportunities for text mining in the FlyBase genetic literature curation workflow.
Database 2012:bas039. [FBrf0219955]


Gene Ontology Consortium (2012).
Gene Ontology annotations and resources.
Nucleic Acids Res. 41(Database issue):D530-5. doi: 10.1093/nar/gks1050. PubMed PMID: 23161678; PubMed Central PMCID: PMC3531070.


S.M. Bunt, G.B. Grumbling, H.I. Field, S.J. Marygold, N.H. Brown, G.H. Millburn and the FlyBase Consortium (2012).
Directly e-mailing authors of newly published papers encourages community curation.
Database 2012; doi: 10.1093/database/bas024. [FBrf0218522]


McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium (2012).
FlyBase 101 – the basics of navigating FlyBase.
Nucleic Acids Res. 40 (Database issue):D706-14. [FBrf0217108]


Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X, Davis P, Tuli MA, Marygold S, Millburn G, Matthews B, Zhang H, Brown N, Gelbart WM, Sternberg PW (2012).
Automatic categorization of diverse experimental information in the bioscience literature.
BMC Bioinformatics. 13(1):16. [FBrf0218533]


Gene Ontology Consortium (2012).
The Gene Ontology: enhancements for 2011.
Nucleic Acids Res. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. PubMed PMID: 22102568; PubMed Central PMCID: PMC3245151.


A. Rangarajan, T. Schedl, K. Yook, J. Chan, S. Haenel, L. Otis, S. Faelten, T. DePellegrin‑Connelly, R. Isaacson, M.S. Skrzypek, S.J. Marygold, R. Stefancsik, J.M. Cherry, P.W. Sternberg, H‑M. Müller (2011).
Toward an interactive article: integrating journals and biological databases.
BMC Bioinformatics 2011, 12:175. [FBrf0214821]


Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011).
The representation of heart development in the gene ontology.
Dev Biol. 354(1):9-17. doi: 10.1016/j.ydbio.2011.03.011. PubMed PMID: 21419760; PubMed Central PMCID: PMC3302178.


Gene Ontology Consortium (2009).
The Gene Ontology in 2010: extensions and refinements.
Nucleic Acids Res. 38(Database issue):D331-5. doi: 10.1093/nar/gkp1018. PubMed PMID: 19920128; PubMed Central PMCID: PMC2808930.


Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B (2009).
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.
Nucleic Acids Res. 38(Database issue):D443-7. doi: 10.1093/nar/gkp910. PubMed PMID: 19884132; PubMed Central PMCID: PMC2808907. [FBrf0209611]


S. St. Pierre, P. McQuilton (2009).
Inside FlyBase (Biocuration as a career).
Fly (Austin). 2009 Jan-Mar; 3(1): 112-114. [FBrf0213427]


Reference Genome Group of the Gene Ontology Consortium (2009).
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
PLoS Comput Biol. 5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3. PubMed PMID: 19578431; PubMed Central PMCID: PMC2699109.


S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi‑Sutherland, A. Schroeder, R. Seal, H. Zhang, and The FlyBase Consortium, (2009).
FlyBase: enhancing Drosophila Gene Ontology annotations.
Nucleic Acids Res. 37: D555-D559; doi:10.1093/nar/gkn788. [FBrf0206621]


Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E (2009).
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
BMC Bioinformatics. 10:59. doi: 10.1186/1471-2105-10-59. PubMed PMID: 19210778; PubMed Central PMCID: PMC2648944. [FBrf0207486]


R. Drysdale, and The FlyBase Consortium, (2008).
FlyBase : a database for the Drosophila research community.
Methods Molec. Biol. 420: 45-59. [FBrf0205804]


Howe, Doug; Costanzo, Maria; Fey, Petra; Gojobori, Takashi; Hannick, Linda; Hide, Winston; Hill, David P.; Kania, Renate; Schaeffer, Mary; St Pierre, Susan; Twigger, Simon; White, Owen; Yon Rhee, Seung (2008).
Big data: The future of biocuration.
Nature. 455(7209):47-50. doi: 10.1038/455047a. PubMed PMID: 19182544; PubMed Central PMCID: PMC2819144. [FBrf0213427]


N. Karamanis, R. Seal, I. Lewin, P. McQuilton, A. Vlachos, C. Gasperin, R. Drysdale, T. Briscoe, (2008).
Natural language processing in aid of FlyBase curators.
BMC Bioinformatics Apr 14; 9:193. PMID: 18410678. [FBrf0206381]


R.J. Wilson, J.L. Goodman, V.B. Strelets, and the FlyBase Consortium, (2008).
FlyBase: integration and improvements to query tools.
Nucleic Acids Res. 36: D588-D593; doi:10.1093/nar/gkm930. [FBrf0203012]


M.A. Crosby, J.L. Goodman, V.B. Strelets, P. Zhang, W.M Gelbart, and the FlyBase Consortium, (2007).
FlyBase: genomes by the dozen.
Nucleic Acids Res. 35: D486-D491; doi:10.1093/nar/gkl827. [FBrf0194786]


Drosophila 12 Genomes Consortium., (2007).
Evolution of genes and genomes on the Drosophila phylogeny.
Nature 450: 203-218. [FBrf0200326]


N. Karamanis, I. Lewin, R. Seal, R. Drysdale, E. Briscoe, (2007).
Integrating natural language processing with FlyBase curation.
Pac Symp Biocomput. 2007;:245-56. [FBrf0206379]


M.F. Lin, et al., (2007).
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
Genome Res 17: 1823-1836. [FBrf0202906]


C.J. Mungall, D.B. Emmert, and the FlyBase Consortium, (2007).
A Chado case study: an ontology-based modular schema for representing genome-associated biological information.
Bioinformatics 23: i337-346. [FBrf0201050]


A. Stark et al., (2007).
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Nature 450: 219-232. [FBrf0200674]


G. Grumbling, V. Strelets and The FlyBase Consortium, (2006).
FlyBase: anatomical data, images and queries.
Nucleic Acids Res., 34: D484-D488; doi:10.1093/nar/gkj068. [FBrf0191339]


R.A. Drysdale, M.A. Crosby and the FlyBase Consortium, (2005).
FlyBase : Genes and gene models.
Nucleic Acids Res., 33: D390-D395 PDF [ 1 Mb, 10-Jan-05] [FBrf0184221]
(Reproduced with permission from NAR Online )


S. Richards et al., (2005).
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
Genome Res., 15: 1-18. [FBrf0184012]


P. Zhou, D. Emmert, P. Zhang, (2005).
Using chado to store genome annotation data.
Current Protocols in Bioinformatics, Vol. 2, pp. 9.6.1-9.6.28. [FBrf0206380]


The FlyBase Consortium, (2003).
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res., 31:172--175 pdf [ 62 kb] .. html [ 21 kb, 16-Dec-03] [FBrf0159266]
(Reproduced with permission from NAR Online )


Rachel Drysdale, (2003).
The Drosophila melanogaster genome sequencing and annotation projects: A status report.
Briefings in Functional Genomics and Proteomics, 2(2): 128--134. PDF [ 100 kb, 26-Jul-03] [FBrf0167361]
(Reproduced with permission from Briefings in Functional Genomics and Proteomics)


Genome Annotation, (2002)


CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin and SE Lewis. (2002).
An integrated computational pipeline and database to support whole-genome sequence annotation.
Genome Biology, 3:research0081 [html] [PDF] [FBrf0155825]


SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall and ME Clamp. (2002).
Apollo: a sequence annotation editor.
Genome Biology, 3:research0082 [html] [PDF] [FBrf0155826]


S Misra, MA Crosby, CJ Mungall, BB Matthews, KS Campbell, P Hradecky, Y Huang, JS Kaminker, GH Millburn, SE Prochnik, CD Smith, JL Tupy, EJ Whitfield, L Bayraktaroglu, BP Berman, BR Bettencourt, SE Celniker, ADNJ de Grey, RA Drysdale, NL Harris, J Richter, S Russo, AJ Schroeder, SQ Shu, M Stapleton, C Yamada, M Ashburner, WM Gelbart, GM Rubin and SE Lewis. (2002).
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
Genome Biology, 3:research0083 [html] [PDF] [FBrf0155827]


The FlyBase Consortium, (2002).
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res., 30:106-108 pdf [ 67 kb] .. html [ 20 kb, 15-Apr-02] [FBrf0141697]
(Reproduced with permission from NAR Online )


K. Matthews and K. Cook (2001).
Genetic Information Online: A Brief Introduction to FlyBase and Other Organismal Databases.
In Encyclopedia of Genetics, E.C.R. Reeve, ed. Fitzroy Dearborn Publishers, Chicago. [FBrf0185967]


Rachel Drysdale, (2001).
Phenotypic data in FlyBase.
Briefings in Bioinformatics, 2(1): 68-80 pdf [ 476 kb, 28-Mar-01] [FBrf0137187]
(Reproduced with permission from Briefings in Bioinformatics)


FlyBase (1999).
FlyBase: Genomic and post-genomic viewpoints.
In S. Letovsky (Ed.)
Bioinformatics: Databases and Systems 141--150. [FBrf0111589]


The FlyBase Consortium, (1999).
The FlyBase Database of the Drosophila Genome Projects and community literature.
Nucleic Acids Res., 27:85-88 pdf [ 34 kb] .. html [ 29 kb, 10-Feb-99] [FBrf0107356]
(Reproduced with permission from NAR Online )


The FlyBase Consortium (1998).
FlyBase - A Drosophila database.
Nucleic Acids Res., 26:85-88 [FBrf0100346]


The FlyBase Consortium (1997).
FlyBase - A Drosophila database.
Nucleic Acids Res., 25:63-66 [FBrf0093096]


The FlyBase Consortium (1996).
FlyBase - The Drosophila database.
Nucleic Acids Res., 24:53-56 [FBrf0085043]


The FlyBase Consortium (1995).
Proposed genetic nomenclature for Drosophila melanogaster.
Trends in Genetics: Genetic Nomenclature Guide, pp.26--29. [FBrf0078422]


The FlyBase Consortium (1994).
FlyBase - The Drosophila database.
Nucleic Acids Res., 22:3456-3458 [FBrf0077015]


M. Ashburner and R. Drysdale (1994).
FlyBase - The Drosophila genetic database.
Development 120:2077-2079 [FBrf0072526]


M. Ashburner (1993).
FlyBase.
GNome News 13:19-20. [FBrf0058642]

Citing FlyBase

We suggest FlyBase be referenced in publications in the following manner:

S.J. Marygold, P.C. Leyland, R.L. Seal, J.L. Goodman, J.R. Thurmond, V.B. Strelets, R.J. Wilson and the FlyBase Consortium (2013). FlyBase: improvements to the bibliography. Nucleic Acids Res. 41(D1):D751-D757. [FBrf0220350]:

FlyBase Copyright

The Copyright of FlyBase

Copyright ©1993-2006 by The Genetics Society of America. All Rights Reserved.

FlyBase comprises a series of electronic documents and information processing software, the reference copy of which currently resides at the Internet address <ftp://flybase.net/flybase/>.

This publication may be copied for non-commercial, scientific uses by individuals or organizations (including for-profit organizations). FlyBase is freely distributed to the scientific community on the understanding that it will not be used for commercial gain by any organization. Any commercial use of this publication, or any parts thereof, is expressly prohibited without permission in writing from the FlyBase consortium.

Certain portions of FlyBase are copyrighted separately. This notice does not invalidate any prior copyright pertaining to portions of FlyBase. Warranty

FlyBase and the Genetics Society of America make no warranty of any kind with respect to the subject matter included herein. FlyBase and the Genetics Society of America specifically disclaim all warranties, expressed, implied or otherwise, including without limitation, all warranties of merchantability, fitness for a particular purpose, or non-infringement.

The information contained in this publication is subject to change without notice.

By viewing or using this information the user agrees that in no event shall FlyBase or the Genetics Society of America be liable for any special, incidental, indirect, or consequential damages of any kind, or any damages whatsoever, whether or not advised of the possibility of damage, arising out of or in connection with the use or performance of this information. Disclaimer

Information in FlyBase is curated from the scientific literature, including unrefereed sources such as abstracts, reviews, and personal communications. With the partial exception of map data, statements of fact are not vetted by FlyBase. Users should remember that published information is not always correct information and are encouraged to use FlyBase as a guide to the literature rather than as a substitute for it.

BIOSIS Copyright

The following statement is with respect to the copyright of bibliographic entries taken from BIOSIS:

"This database is copyrighted by Biological Abstracts Inc. (BIOSIS®). All rights reserved. No part of the information may be reproduced in hard copy, machine-readable form or other form without advance written permission from BIOSIS. Information has been obtained from public sources believed to be reliable. BIOSIS makes a diligent effort to provide complete and accurate representation of the bioscientific and other literature in its publications and services. However, BIOSIS does not guarantee the accuracy, adequacy, or completeness of any information and BIOSIS makes no warranties or representations of any kind, express or implied, including but not limited to warranties of merchantability or fitness for particular purpose. BIOSIS disclaims all liability for errors or omissions that may exist and shall not be liable for any incidental, consequential or other damages (whether resulting from negligence or otherwise) including, without limitation, exemplary damages or lost profits arising out of or in connection with the use of this database. Errors or omissions may be reported to Biological Abstracts Inc., 2100 Arch Street, Philadelphia, PA 19103-1399."

Herskowitz's Bibliography Copyright

The following statements are with respect to the copyright of Parts 5 and 6 of Herskowitz's bibliography:

"Bibliography on the genetics of Drosophila: Part 5, by Irwin H. Herskowitz is reproduced with the permission of Macmillan Publishing Company. Copyright ©1969 by Macmillan Publishing Company. "

"Bibliography on the genetics of Drosophila: Part 6, by Irwin H. Herskowitz is reproduced with the permission of Macmillan Publishing Company. Copyright ©1974 by Macmillan Publishing Company."

Lindsley and Zimm (1992)

Lindsley and Zimm (1992) - The New Redbook The Genome of Drosophila melanogaster Dan L. Lindsley & Georgianna G. Zimm Copyright 1992 By Academic Press, Inc. All Rights Reserved.

ISBN 0-12-450990-8 Academic Press, Inc. 1250 Sixth Avenue, San Diego, California 92101-4311

FlyBase is based on the information contained in Lindsley and Zimm's The Genome of Drosophila melanogaster (Academic Press, 1992), however we no longer redistribute the complete text of the book.

FlyBase Data Sources

The Red Book

Bibliographies

External Databases

Journal Articles and Books

Drosophila Conference Abstracts

Personal Communications to FlyBase

Direct Submission of High-Throughput Data

Insertion Collection Data

Stock Lists Submitted to FlyBase

People

FlyBase Alumni

FlyBase thanks these former members of the FlyBase consortium for their contribution: 

   Manish Anand
   Michael Ashburner
   Leyla Bayraktaroglu
   Ben Berman
   Brian Bettencourt
   Lee Bitsoi
   Pete Brokstein
   Stephanie Bunt
   Heather Butler
   Kathy Campbell
   Russell Collins
   Kim Cook
   Anthony DeAngelo
   Aubrey de Grey
   Rachel Drysdale
   Helen Field
   Rebecca Foulger
   Erwin Frise
   Mark Gibson
   Don Gilbert
   Janet Gulotta
   Cyrus Harmon
   Nomi Harris
   Gregg Helt
   Pavel Hradecky
   Yanmei Huang
   Josh Kaminker
   Kerry Knight
   Sophia Kossida
   Rob Kulathinal
   Julia Lamenza
   Joe Lemaire
   Stan Letovsky
   Suzanna Lewis
   Paul Leyland
   Guo-chun Liao
   Anne Loraine
   Glenn McAlpine
   John Merriam
   Sima Misra
   Emanuel Mongin
   Chris Mungall
   Tatiana Murnikova
   Catherine Nelson
   Dawn Palmer
   Simon Prochnik
   Simon Reeve
   John Richter
   Wayne Rindone
   Margo Roark
   Gerry Rubin
   Ruth Seal
   Carolyn Shemen
   Hardik Sheth
   Nihar Sheth
   Shengqiang Shu
   David Simas
   Chris Smith
   Frank Smutniak
   Jon Tupy
   Edwin Wang
   Eddy Wellbourne
   Eleanor Whitfield
   Colin Wiel
   Mark Williams
   Robert Wilson
   J.D. Wong
   Chihiro Yamada
   Mark Yandell
   Haiyan Zhang
   Peili Zhang

FlyBase Support

FlyBase is supported by a grant from the National Human Genome Research Institute at the U.S. National Institutes of Health #P41 HG000739.

Support is also provided by the British Medical Research Council and the Indiana Genomics Initiative.

Hosting of this site is supported in part by the National Science Foundation (#OCI-1053575) through XSEDE resources provided by Indiana University.

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